Method and apparatus for rapid detection of bacterial contamination

ABSTRACT

A device and method for detecting the presence of bacteria in a sample are provided. A multi-step process for sample preparation is utilized and a microfluidic device is disclosed. The detection is performed using microfluidics and physical changes in multiple samples in differential mode.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is filed under the provisions of 35 U.S.C. § 121 and isa divisional of U.S. patent application Ser. No. 16/000,935 filed onJun. 6, 2018, now U.S. Pat. No. 10,948,414, which claims priority toU.S. Provisional Patent Application No. 62/515,598 filed on Jun. 6, 2017in the name of Mustafa Al-Adhami and entitled “Method and Apparatus forRapid Detection of Bacterial Contamination,” which are herebyincorporated by reference herein in their entirety.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH

Portions of this invention may have been financially supported by theUnited States Government support under a grant from the U.S. Food & DrugAdministration under Grant Number UO1-MD-0022012.

FIELD

The present invention relates to a method of detecting the presence ofviable cells in a sample, and a device that is useful for saiddetection. Advantageously, the device is microfluidic and as such, thesystem for detecting the presence of viable cells can be compact,portable, and/or hand-held and permits the user to identify if viablecells (e.g., microorganisms) are present in the sample within minutes.

BACKGROUND OF THE INVENTION

Each year, thousands of people die and millions are sickened due tofood, water, or medicine contamination [1]. In order to prevent most ofthese poisonings, a rapid, precise and sensitive microbial detectionmethod is highly desirable [2,3]. There are many common methods todetect pathogens and other biologics [4]. Most of these methods requirewell-equipped and environmentally stable laboratories as well as highlytrained staff to handle devices and reagents or antibodies [4]. Thesemethods are hard to apply in the field, especially for products thathave to be sterile to prevent infection of the patients [1,5]. For manyindustries, the late detection of contamination can be costly.Therefore, it is vitally important to develop a method and apparatusthat can detect contamination rapidly and is robust enough to utilize inthe field. Detecting the contamination at an early stage can save bothtime and labor for the manufacturer and more importantly, increases thesafety of the final product. For example, having near-real-time feedbackof possible contamination in bioreactors can be very critical since eachbatch takes many days to grow before harvest and it would be of greatinterest to abort the process early in case of contamination [6]. Thedevice could be used for multiple applications, some of which aredescribed below.

A proposed application of rapid microbial detection is in the qualitycontrol processes for biopharmaceuticals. Since biologics are highlysusceptible to contamination by adventitious agents such as viruses ormycoplasma, there is a need for risk mitigation procedures such astesting to confirm the absence of any unwanted contaminants [7]. Thisway, contaminated products can be caught early, which minimizes the riskof having them produced and then sold in pharmacies. Furthermore, rapidmicrobial detection could be used during the biological process to testmanufactured drugs for contamination [8].

Cholera is an acute infection caused by the ingestion of food or watercontaminated with the bacterium Vibrio Cholerae. It has been estimatedthat each year there are 1.3-4.0 million cases of cholera, withapproximately 100,000 deaths. The incubation period of the cholerabacteria is 12 hours to 5 days. In severe cases, cholera can kill aperson within an hour of showing symptoms. It can be hard to diagnose apatient with cholera since the symptoms are similar to other diseases,for example acute watery diarrhea. However, it is very important todetect cholera early because of the potential for a widespread outbreak.The best way to prevent cholera is to detect it in water before itenters the body. Traditionally, to test for water sterility, all waterspecimens have been collected in temperature-controlled containers andtransported to a laboratory. Large volumes of water are needed forbetter pathogen detection. The most common way to detect thecontamination is by direct cell culture, wherein the contaminated sampleis diluted with alkaline peptone water (APW), incubated at 35° to 37°C., and then plated for 6-8 hours. Alternatively, 100-300 mL of watersample is filtered through 0.22-0.45 μm membrane (Millipore) filters andthen the filter placed in 100 mL of APW in a flask. The sample is thenincubated for 6-8 hours and then plated for 18 to 24 hours at 35° to 37°C. Accordingly, most assays to detect cholera in water samples are timeconsuming, expensive, and require highly trained lab technicians, andare not sensitive enough to detect low concentrations of bacterialcontaminants. Moreover, the current methods of detecting cholera are notuseful in the field where rapid and reliable cholera detection is mostneeded. A portable device that can timely and sensitively detect thepresence or absence of Vibrio Cholerae in water samples is thereforeneeded to prevent cholera from spreading, especially in regions withlimited or no laboratories.

In some infections, for example sepsis, evidence of contamination can bedelayed, resulting in an increased risk of developing septic shock,which is associated with high mortality rates. Sepsis usually affectsthe young, the old, and those with a weak immune system. When a patientis determined to have sepsis, there is a response bundle that medicalprofessionals follow to fight against the infection. The key to fightingsepsis is to start antibiotics early. Broad spectrum antibiotics areusually prescribed to these patients to cover all likely pathogens whileblood samples are being tested. Preferably, a method of contaminationdetection will allow for the rapid determination of the sepsis infectionso that the best antibiotic can be prescribed immediately.

Presently, “rapid” methods of contamination detection take approximately24 hours. For example, in the case of the polymerase chain reaction(PCR), it has been stated in the protocol that it can be used to detectthe viable cells present only in the exponential phase. PCR is verylabor intensive and takes approximately 27 hours to achieve results.Although PCR can detect contamination of colony forming units as low as10 CFU, it is not clear whether the detected cells are dead or alive atthe time of detection. There are other reported methods that are faster,for example measuring the intrinsic fluorescence of the bacterial oryeast chromophores [9]. This approach is fast and sensitive but it islimited to a slightly higher number of colony forming units and it isvery specific, requiring a high level of knowledge about the environmentin which the contamination is detected to compensate for backgroundsignal.

Additionally, other properties that can be monitored to determine themetabolic rate of viable cells include pressure, pH, carbon dioxidedetection, fluorescence, and absorbance. Negative pressure detection inenclosed containers has been used to detect bacteria, in whichelectronic transducers are used. Another way is by using pH sensitivehydrogels inside cuvettes where the bacterial growth is correlated tothe pH changes in the system. Detecting the level of CO₂ in the mediumis also a way to determine the metabolic rate. Indicator dyes could alsobe used to detect the metabolic rate of bacteria. Indicator dyes arealso used to detect viable cells in samples where fluorescence orabsorbance is monitored.

There remains the need in the art of contamination detection for adevice and a method of using same that is able to detect the presence ofviable cells in samples rapidly. This device may be compact, portable,and/or hand-held, and may detect changes in fluorescence, absorbance,temperature, pressure, pH, conductivity and/or image processing using amobile phone, tablet, or computer.

SUMMARY OF THE INVENTION

In a first aspect, a microfluidic cassette is described, said cassettecomprising:

at least two channels, wherein a first channel is communicativelyconnected to a first chamber and a second channel is communicativelyconnected to a second chamber, wherein the cassette further comprises atleast one inlet injection port and each channel has a dedicated outletinjection port, wherein each injection port has a septum.

In another aspect, a kinetic fluorometer system is described, saidsystem comprising:

an excitation module comprising a light source and a voltage-controlledcurrent source;

a microfluidic cassette;

an excitation filter mounted between the light source and themicrofluidic cassette;

a detector positioned 90° relative to the excitation light path from thelight source;

an emission filter positioned between the detector and the microfluidiccassette; and

a microprocessor.

In still another aspect, a method of detecting the presence of viablecells in a sample is described, said method comprising detecting aphysical property of a sample and a sample-derived negative control andcomparing same to determine a differential rate, wherein thedifferential rate is indicative of the presence of viable cells in thesample.

Other aspects, features and embodiments of the invention will be morefully apparent from the ensuing disclosure and appended claims.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1A illustrates the reduction of resazurin to resorufin.

FIG. 1B illustrates the color transformation when resazurin is convertedto resorufin.

FIG. 2 illustrates the excitation and emission paths relative to themicrofluidic cassette in the kinetic fluorometer.

FIG. 3 is a schematic of one embodiment of the microfluidic device ofthe invention.

FIG. 4 is a schematic of another embodiment of the microfluidic deviceof the invention.

FIG. 5 is a schematic of still another embodiment of the microfluidicdevice of the invention.

FIG. 6 shows the results of the sample relative to the sample-derivednegative control from Example 1.

FIG. 7 illustrates the importance of having a sample derived negativecontrol by comparing the fluorescence intensity of filtered versusnon-filtered Kombucha tea.

DETAILED DESCRIPTION, AND PREFERRED EMBODIMENTS THEREOF

The present invention relates to a device and method that can detectmicroorganism contamination in samples by detecting the metabolicactivity of viable cells. Advantageously, the device and method allowsthe user to compare the sample to a sample-derived negative controlconcurrently and simultaneously. This device may be compact, portable,and/or hand-held, and may detect changes in fluorescence, absorbance,temperature, pressure, pH, conductivity and/or image processing using amobile phone, tablet, or computer.

As defined herein, a “sample-derived negative control” corresponds tothe sample wherein any viable cells have been inactivated or removed.For example, the cells can be removed using a microfilter orcentrifugation or other microfluidic-based cell separation methods, asreadily understood by the person skilled in the art. Mammalian cells canbe simply sedimented, e.g., left in a container for a period of timewith a blood thinner, e.g., heparin, added to the blood to minimizeclotting. As defined herein, the sample-derived negative control ispreferably substantially devoid of viable cells.

As defined herein, a “sample” corresponds to any material that isaqueous-based. The sample comprises water and may contain othersubstances that are soluble or dispersed in water, e.g., cells,micelles, colloidal material, etc. For example, the sample can befiltered or non-filtered water, treated or non-treated water, urine,blood, plasma, tears, aqueous-based beverages, sewage, animal lagoonwater, pharmaceutical reaction solutions, milk, and any solutionscomprising solubilized pharmaceuticals, contrast agents (X-ray, PET orMRI), radio nuclides, nutraceuticals, or food.

As defined herein, “cells” can include prokaryotic cells (e.g.,pathogenic bacteria) and eukaryotic cells (e.g., pathogenic tumorcells).

Microorganisms that can be detected using the device and methoddescribed herein include, but are not limited to, Escherichia coli,Listeria monocytogenes, Salmonella species (e.g., S. typhi), Vibriocholera, Shigella (e.g. S. dysenteriae), Cryptosporidium parvum,Toxoplasma gondii, Giardia lamblia, Cyclospora cayetanensis; Pseudomonas(e.g., P. aeruginosa, P. putida), Bacillus, Clostridium (e.g., C.botulinum, C. tetani, C. difficile, C. perfringens), Corynebacterium(e.g., C. diphtheria), Arthrobacter, Lactobacillus, Microbacterium,Micrococcus, Streptococcus (e.g., S. pyogenes, S. pneumoniae), Listeria,Escherichia, Yersinia (e.g., Y. pestis), Campylobacter, Mycobacterium(e.g., M. tuberculosis, M leprae), Staphylococcus (e.g., S. aureus),Haemophilus (e.g., H. influenza), Neisseria (e.g., N. meningitidis, N.gonorrhoeae), Chlamydia (e.g., C. trachomatis), Bordetella (e.g., B.pertussis), Treponema (e.g., T. palladiu), and combinations thereof.

Depending on the sample studied, there are multiple ways in which viablecells are detected. Traditionally, a cell culture is required for mosthuman-related samples wherein cells are grown under controlledconditions. Most of these methods are done in laboratories and requirecareful handling. Most cell cultures go through two important steps;cell isolation wherein the cells are extracted from the sample and cellmaintenance in a culture. It is also important to monitor conditionsinside the culture in case there is a change in pH levels and/ornutrient depletion. For non-human-related samples, there are devicesthat can detect contamination. Most of these devices can take upwards of24 hours to analyze the samples.

What is needed is a rapid, robust, cost effective, and non-invasivedevice to detect metabolic changes of viable cells in samples with highsensitivity to detect low levels of contaminations and/or early stagesof infections. An aspect of the device is to have a sample-derivednegative control so that both the positive and negative control samplesare measured simultaneously such that any difference between the twosamples determines the presence of viable cells. The sample-derivednegative control is created from the sample by splitting it in twoportions and removing the bacteria (e.g. by filtering, centrifuging,etc.) from one of the portions. Both the sample and the sample-derivednegative control are loaded at the same time in separate microfluidicchambers, mixed with the same amount of indicator dye, and kept at thesame conditions (e.g., temperature, pressure, etc.). The difference inthe conversion rates of Resazurin, termed differential rate, ismonitored. By using the differential rate, it is possible to test anytype of sample regardless of the medium, while removing the effects ofpossible interfering substances. Advantageously, the device and methoddoes not rely on the use of traditional plate-based assay tests toverify the results.

Broadly, a microfluidic device and method of using same is described,wherein the microfluidic device has two channels, one for unalteredsample and one for the sample-derived negative control, wherein eachchannel is communicatively connected to at least one dedicated chamber.The method uses the difference in at least one physical property betweenthe sample and the sample-derived negative control to detect thepresence of viable cells (i.e., the metabolic activity of the sample) inthe sample. The device may detect changes in fluorescence, absorbance,temperature, pressure, pi, conductivity and/or image processing in thesample and then compare it to the sample-derived negative control. Thedevice provides for the reliable detection of contamination in less thanabout 30 minutes.

The device does not identify the species or the growth phase of thecells that are detected. The main purpose of the device is to detectviable cells in the tested samples. Having the ability to rapidly screena variety of samples irrespective of the contaminating species is ofgreat value to many industries and municipalities. The device and methodhave proven to be accurate and fast, which makes it suitable for rapiddetection of contamination applications.

It should be appreciated by the person skilled in the art that the timeof the measurement of the at least one physical property can bevariable, from time in a range from about 1 minute to about 240 minutes,preferably from about 1 minute to about 30 minutes for a vigorouslygrowing aerobe and about 60 minutes to about 240 minutes for barelyviable, low respiration rate cells.

In one aspect, a microfluidic cassette is described, said microfluidiccassette comprising: at least two channels, wherein a first channel iscommunicatively connected to a first chamber and a second channel iscommunicatively connected to a second chamber, wherein the cassettefurther comprises at least one inlet injection port and each channel hasa dedicated outlet injection port, wherein each injection port has aseptum.

As will be described below in the examples, the microfluidic cassettecan comprise a fork defining the first channel and the second channelsubsequent to the inlet injection port, or can comprise a first inletinjection port for the first channel and a second inlet injection portfor the second channel.

Ina second aspect, a kinetic fluorometer system is described, saidsystem comprising:

an excitation module comprising a light source and a voltage-controlledcurrent source;

a microfluidic cassette;

an excitation filter mounted between the light source and themicrofluidic cassette;

a detector positioned 90° relative to the excitation light path from thelight source;

an emission filter positioned between the detector and the microfluidiccassette; and

a microprocessor.

The microfluidic cassette described herein can be used in the kineticfluorometer system or alternatively, a different microfluidic cassettecan be used in said fluorometer system.

In a third aspect, a method of detecting the presence of viable cells ina sample is described, said method comprising detecting a physicalproperty of a sample and a sample-derived negative control and comparingsame to determine a differential rate, wherein the differential rate isindicative of the presence of viable cells in the sample. The methodfurther comprises loading the sample and the sample-derived negativecontrol in a microfluidic cassette, wherein the microfluidic cassettedescribed herein can be used in the method of detecting oralternatively, a different microfluidic cassette can be used in saidmethod, so long as there are two separate chambers for detectingphysical properties of the sample and the sample-derived negativecontrol in the microfluidic cassette. Advantageously, if the sample hasbeen prepared to include an increase in a concentration of viable cellstherein, there is an increased sensitivity of the detecting of thepresence of viable cells in the sample.

Recently, resazurin has been found to be an inexpensive compound thatcan provide a fluorescent readout at good sensitivity [10, 11].Resazurin is a blue dye which itself is weakly fluorescent [10].However, viable cells retain the ability to reduce resazurin intoresorufin, which is highly fluorescent [11]. Nonviable cells do not havethe metabolic capacity to reduce this indicator dye. Resazurin-basedassays are used for viability detection of cells other than bacterialcells, e.g., human cells for clinical transplantation [12], stem cells[13], CD4 T cells [14], and malarial gametocytocidal assay [15]. Also,resazurin-based assays can be used for the screening of bacteria forradiation sensitivity [16].

As shown in FIG. 1 , the conversion of resazurin to resorufin changesthe color of the dye from blue to red, which is accompanied by asignificant increase of the absorption green-yellow-green region ofvisible light (λ_(max)=570 nm). The fluorescence emission in theorange-red region (λ_(max)=590 nm) is enhanced as well. The conversionprocess provides a linear curve over a wide range of cell concentrations[17]. Accordingly, in one embodiment, the viable cells are detected inthe sample using resazurin and fluorescence detection.

Advantageously, the method of use includes, but is not limited to, (i)may provide health-care facilities with a means to determine the rightantibiotic to prescribe for patients suffering from differentinfections, e.g., sepsis, (ii) may be used to detect contamination inwater samples, e.g., the presence of cholera, (iii) may be used todetect probiotics in food such as yogurt, (iv) may be used to detectfood spoilers, e.g., Lamellae bacteria, and (v) may be used to detectcontamination in pharmaceutical products. The device may or may not needa power source depending on the operating mode. It may be automatic orbe run manually. The device may or may not be a single-use kit dependingon the materials used.

Accordingly, in another aspect, a method of testing the efficacy ofantibiotics is described, said method comprising detecting a physicalproperty of (i) a sample in the presence of an antibiotic and (ii) asample-derived negative control and comparing same to determine adifferential rate, wherein a differential rate is indicative of thereduced or negligible efficacy of the antibiotic on the sample. In otherwords, if the antibiotic was able to kill the cells, the slope of thesample in the presence of antibiotic should be substantially zero,similar to that of the negative control. The method comprises loadingthe sample and the sample-derived negative control in a microfluidiccassette, wherein the microfluidic cassette described herein can be usedin the method of detecting or alternatively, a different microfluidiccassette can be used in said method, so long as there are two separatechambers for detecting physical properties of the sample and thesample-derived negative control in the microfluidic cassette.

In yet another aspect, the system can be used in a method ofdistinguishing between antibiotic resistant and non-resistant bacterialstrains, wherein if the putative bacteria are resistant, they will showviability even in the presence of the tested antibiotic, while thecontrol bacteria will die. In this method, a physical property of (i) aviable sample in the presence of an antibiotic and (ii) an antibioticresistant sample in the presence of the antibiotic are measured andcompared to determine a differential rate, wherein a differential rateis indicative of the an antibiotic resistant sample. In this case, thedifferential rate is a negative slope, wherein the viable sample has alower slope compared to the antibiotic resistant control. The methodcomprises loading the viable sample and the antibiotic resistant samplein a microfluidic cassette, wherein the microfluidic cassette describedherein can be used in the method of detecting or alternatively, adifferent microfluidic cassette can be used in said method, so long asthere are two separate chambers for detecting physical properties of thesample and the sample-derived negative control in the microfluidiccassette.

In another aspect, a method of determining the dose response of a strainof bacteria to an antibiotic is described, wherein the dose that kills aprescribed percentage of the bacteria is readily determined using themicrofluidic cassette described herein. Being able to prescribe thecorrect antibiotic in the correct dose is important, as it allows todecrease the chance of developing antibiotic resistance. Prescribing theminimum needed dose to achieve the maximum effect plays an importantrole in the antibiotic stewardship.

In still another aspect, a method of detecting contamination in water,food, or pharmaceutical products, by-products, or intermediates isdescribed, said method comprising detecting a physical property of asample and a sample-derived negative control and comparing same todetermine a differential rate, wherein the differential rate isindicative of the presence of viable cells or contamination in thesample. The sample comprises the water, food or pharmaceutical products,by-products, or intermediates to be tested.

In yet another aspect, a method of detecting probiotics in water or foodis described, said method comprising detecting a physical property of asample and a sample-derived negative control and comparing same todetermine a differential rate, wherein the differential rate isindicative of the presence of viable cells in the sample.

The features and advantages of the invention are more fully illustratedby the following non-limiting examples, wherein all parts andpercentages are by weight, unless otherwise expressly stated.

EXAMPLE 1

Proof of Concept

The device prototype used as a proof of concept is a portable devicethat consists of two single-excitation, single-emission photometers, onefor the sample and another for the sample-derived negative control. Thephotometers continuously measure fluorescence intensity of an indicatordye and provides a plot of same. The slope of the plot depends on thenumber of colony forming units per milliliter of sample. The method anddevice utilize resazurin as the indicator dye wherein any viable cellspresent in the sample reduce resazurin to resorufin, which is morefluorescent. Photodiodes were used to detect fluorescence change. Thephotodiode generated current proportional to the intensity of the lightthat reached it, and an op-amp was used in a transimpedance differentialconfiguration to ensure amplification of the photodiode's signal. Amicrofluidic chip was designed specifically for the device. It acts as afully enclosed cuvette/cassette, which enhances the resazurin reductionrate. In tests, the E. coli-containing media were injected into themicrofluidic chip and the device was able to detect the presence of E.coli in LB media based on the fluorescence change that occurred in theindicator dye. The various components of the device and process areintroduced below.

Portable Kinetic Fluorometer

The kinetics fluorometer is a single-excitation, single emissionphotometer that can detect fluorescence change in two samples and thenplots the readings. A generalized schematic of the excitation module 10of the device is shown in FIG. 2 . The excitation 25 and emission 55light paths are oriented at 90° at each other. The excitation module 10consists of a light source, e.g., an LED, laser-diode,electroluminescent lamp, incandescent lamp, halogen lamp, sunlight, orother light source, with emission maximum of 525 nm and voltagecontrolled current source (not shown) which sets a constant currentthrough the light source. An excitation filter 30 is mounted in front ofthe light source 20 in order to filter all the light that enters themicrofluidic cassette 40. Ideally, the filter 30 and the light source 20should be mounted in a holder that keeps them mechanically aligned. Theholder is preferably made of non-fluorescent materials, A photodiode 60is employed to detect the fluorescence intensity by generating currentproportional to the intensity of the light reaching them. The photodiodeshould be mounted at an angle of 90 degrees to the excitation beam, withthe emission filter 50 mounted in front of it. It should be appreciatedthat the detector should be chosen based on the physical propertymeasured and in the present description is specific to fluorescence. Thesample is loaded into the device via the microfluidic cassette 40.

Strong ambient light may interfere with device operation, even though itcan be shielded (e.g., the cassette holder can be made of blackplastic). Care should be taken to avoid placing it close to room lights.

It should be appreciated by the person skilled in the art that althoughthe discussion relates to a portable kinetic fluorometer, it is easilyenvisioned that the microfluidic cassettes and method described hereincan be used on a kinetic fluorometer in a laboratory. Further, it iseasily envisioned that sunlight can be used as the light source and ifthe detector is a solar cell detector, a totally passive device thatdoes not use battery power can be created that is still capable of anopto-electronic measurement.

Microfluidic Cassettes

Essentially, the cassette includes: a) separate chambers for cell-ladenand cell-free sample; and b) the chambers must be monitored in a suchway that there is no cross-talk, i.e., light exiting one of the chambersmust not reach the photodetector for the second chamber. If thishappens, it distorts the results (non-linear slopes) and decreasessensitivity. This could be avoided by introducing light barriers betweenthe chambers.

The microfluidic cassette is a fully enclosed acrylic cuvette. Thecuvette comprises an acrylic sheet where the channels and chambers arecut. In the example, acrylic was used, but it should be appreciated thatany visible range transparent polymer with no or minimal haze can beused provided that it is joined using thermal or pressure (physical)bonding. Adhesive bonding interferes with the indicator so is preferablynot used. In addition to acrylic, other materials that can be usedinclude, but are not limited to, polystyrene, polycarbonate, polyesters,celluloids (e.g., cellulose acetate or similar cellulosic derivatives),and any other thermoplastic or thermoset optical resins. The acrylicsheet can have a depth of about 1 mm to about 3 mm, preferably above 1mm to about 2 mm, and most preferably about 1.5 mm. The acrylic sheet isthen covered on the top and on the bottom with a thin layer of poly(methyl methacrylate) (PMMA) or polystyrene to form a fully enclosedcuvette. The thin layers can be each about 0.2 mm thick. It should beappreciated by the person skilled in the art that the cuvette can be onelayer if 3D printing is used, two layers if the channels are engravedand not cut through from the top to the bottom of the acrylic sheet, oreven more layers if other functions are added. The chemical compositionof the microfluidic cassette is important. Specifically, the “glue” thatis used to attach the acrylic sheet to the PMMA or polystyrene layersmust not react with the indicator and must not deteriorate the opticalquality of the surfaces. Accordingly, adhesives are preferably not usedand the cassette is sealed by pressure, temperature, and weak solventassistance. If PMMA is used in the cuvette, chloroform, acetone orsimilar are to be avoided. The weak solvent used can be ethanol, whichnot only helps to bond the device, but also sterilizes it. Other weaksolvents include, but are not limited to, methanol/water, dimethylsulfoxide/water, ethyl acetate/water. In general, any organic solventsthat do not dissolve the plastic well and evaporate completely duringthe bonding are possible to be used. It should be appreciated that thesolvents used is specific for a given polymer (i.e., PMMA orpolystyrene). The microfluidic cassette can be heat treated to bond thelayers, as readily understood by the person skilled in the art.

The microfluidic cassette of the inventions has two channels, eachchannel leading to at least one chamber, wherein one chamber is for thesample-derived negative control and one chamber is for the sample. Thepresent inventors found that it's important to have a negative controlsince some samples (e.g., samples comprising Vitamin C, caffeine andother samples that react with NADH) might have the same reduction effecton the indicator dye, resulting in a false positive. The differencebetween the change in fluorescence between the sample and thesample-derived negative control correlates to the number of colonyforming units per milliliter in the sample. It should be appreciatedthat although the description of the sample-derived negative control isspecific to fluorescence that the importance of the sample-derivednegative control can be extended to other detection means (e.g.,absorbance, temperature, pressure. pH, conductivity and/or imageprocessing) to eliminate problems with false positives.

A first embodiment of the dual channel microfluidic cassette 40 isillustrated in FIG. 5 . Each channel 200, 210 communicatively connectsto a chamber 250, 260, respectively. Notably, FIG. 5 includes a filter240 in the right channel, but the filter is optional in the cassette ofFIG. 5 , as the sample-derived negative control can be prepared (e.g.,filtered or centrifuged) prior to introduction to channel 210. Thefilter is chosen to capture cells by having pores of about 0.2 micronsor less. The cassette 40 further includes injection ports 220, 230, 270,and 280, wherein the injection ports can be septa ports which can bepierced. Alternatively, the ports can be drilled in the sides of thecassette and filled with silicone, thereby acting like a septum. Themicrofluidic cassette 40 of FIG. 5 is preferably designed so as toprovide air free filling via capillary force. Notably, the embodimentillustrated is FIG. 5 is not intended to limit the device design in anyway and the channels and chambers may be perfected to satisfy the designpreferences. Moreover, it is easily envisioned by the person skilled inthe art that a light barrier can be inserted in the cassette between thechambers to minimize any cross talk between the chambers.

In practice, the cassette 40 of FIG. 5 can be filled by attachingneedles to ports 220 and 270 and injecting the sample into chamber 250,wherein port 270 acts as a vent to minimize air in the cassette. Needlescan be attached to ports 230 and 280 and either (a) a pre-filteredsample-derived negative control can be injected into the chamber 260, or(b) a filter 240 is present in the channel 210 and sample is injectedinto port 230, wherein the filter captures cells such that thesample-derived negative control is generated in chamber 260. Port 280acts as a vent to minimize air in the cassette. Additionally, tominimize bubbles in the chamber, which can lower sensitivity, thechannels preferably have a small cross-section.

Another embodiment of the cassette 40 is shown in FIG. 3 . As indicated,there are two channels 100, 110 in the cassette of the invention,wherein channel 100 communicatively connects to chamber 150 and channel110 communicatively connects to chamber 160, which is communicativelyconnected to chamber 170. In other words, in the embodiment of FIG. 3 ,one of the two channels feeds at least two chambers. Further, themicrofluidic cassette 40 comprises a filter 130 and injection ports 120,140, 180. The filter is chosen to capture cells by having pores of about0.2 microns or less, and the injection ports can be septa ports whichcan be pierced. Alternatively, the ports can be drilled in the sides ofthe cassette and filled with silicone, thereby acting like a septum. Itis easily envisioned by the person skilled in the art that a lightbarrier can be inserted in the cassette between the chambers to minimizeany cross talk between the chambers.

Still another embodiment of the cassette 40 is shown in FIG. 4 . Thecassette of FIG. 4 is almost identical to the cassette of FIG. 3 insteadthere is just one chamber associated with channel 110. It is easilyenvisioned by the person skilled in the art that a light barrier can beinserted in the cassette between the chambers to minimize any cross talkbetween the chambers.

In phase one 190 of the loading of the sample in the microfluidiccassette of FIGS. 3 and 4 , needles are attached to ports 120 and 180and the sample entering at port 120 fills chamber 150 and also passesthrough filter 130 and fills chambers 160 and 170 (or just chamber 170in FIG. 4 ). Any cells that may be in the sample accumulate on the sideof the filter 130 closest to port 120 and as such, the liquid containedin chambers 160 and 170 are cell-free (i.e., bacteria free) and serve asthe sample-derived negative control. In phase two 195, needles or otherpiercing means are attached at ports 180 and 140 and air is injected viaport 180 to “blow” the bacteria back into chamber 150. This method hasthe advantage of doubling or tripling the concentration of cells in thesample in chamber 150 (if any viable cells are present in the sample),thereby increasing the sensitivity of the process.

In general, the experiments performed by the inventors suggest that thethree-chamber cassette of FIG. 3 is more sensitive than the two-chambercassette of FIG. 4 when only one sample is being tested. If the intentis to test more than one sample, the cassette can be adapted to includemore chambers, as readily understood by the person skilled in the art.

Preparation of the Cells

To test the device of FIG. 5 , E. coli cells were used. Initially, 100mL primary culture was prepared using 10 μL of E. coli NM303 cells,which were grown at 37° C. in a shaker at 150 rpm for 8 hours until theoptical density of primary culture was measured to be 2.5 at 600 nm Theprimary seed culture (1%) was used to inoculate 200 mL of secondaryculture grown at 37° C. in a shaker at 150 rpm to reach an opticaldensity of 0.4 at 600 nm. This sample was used for making serialdilutions to get the concentration of 1000 CFU/mL. Then, 1 mL of theresulting solution is mixed with 5 μL of resazurin dye to be tested bythe system. The dye was prepared as previously described by Al-Adhami,M., et al. [18].

Measurement of Resazurin Reduction

1 mL of the cell culture with the respective number of CFU is depositedin an EPPENDORF tube. Then, 3.3 μL of freshly made reaction mix is addedto it and the final mixture is vortexed and 300 μL are injected into themicrofluidic cassette of FIG. 5 . The reaction mix comprises PBS andresazurin stock solution. Two needles are used on the both sides of thecassette. The first needle is used to inject the mix, while the secondneedle serves as a vent for the air. A sample-derived negative controlis also prepared wherein some amount of the final mixture is filteredand the filtrate is injected into the other chamber of the cassette,analogous to how the sample is injected. After withdrawing the needles,the cassette is inserted into the kinetic fluorometer cassette holder.

Once the cassette is in the device, a control program is started (asdiscussed in [18]). It continuously measures and displays thefluorescence intensity. The control program also calculates the runningvalue of the slope of the fluorescence intensity change. If the slope issubstantially zero, there is no contamination. If the slope issignificant, the media is contaminated.

FIG. 6 shows the results of the sample relative to the sample-derivednegative control. It can be seen that the sample-derived negativecontrol has a slope of substantially zero while the sample has apositive slope. By comparing the difference of fluorescence intensitywith time, we are able to correspond the slopes with the number ofviable cells in the sample.

EXAMPLE 2

Kombucha tea was studied to emphasize the importance of the differentialstudy of contamination in samples. Kombucha has caffeine and livecultures in which both are reducing agents. 1 mL of the Kombucha cellculture with the respective number of CFU is deposited into an EPPENDORFtube. Then, 5 μL of the freshly made resazurin dye mix is added to it.The final mixture is mixed and 300 μL are injected into the microfluidiccassette of FIG. 5 and inserted into the kinetic fluorometer cassetteholder. Once the cassette is in the device, the control program isstarted. FIG. 7 shows the importance of having the negative controlembedded into the system. Unlike a regular cell culture, Kombucha yeastis cultured in tea. It is natural for the tea to have caffeine which isa known antioxidant. Antioxidants can cause a similar reaction with theresazurin dye as bacteria. The difference in slopes between the filteredand non-filtered samples determines the presence of contamination.

EXAMPLE 3

The device is also used to automatically detect contamination indrinking water. The fluidic system consists of a 1 L water tank that iscontinuously being stirred and has an outlet at the bottom. The outletis connected to a syringe pump equipped with a 60 mL syringe. Thesyringe pump will pull the water out of the tank to be stored in thesyringe. A second syringe pump containing the LB media/Resazurin mix isprepared. The two pumps run simultaneously and mix via a microfluidicmixer. The mixed sample is then divided into two parts. 1 ml goesthrough a 0.2 μm filter to make sure it doesn't contain bacteria whilethe bacteria containing sample is deposited directly into the readingcuvette. When the sample is loaded into the microfluidic cassette, thedevice will take readings for 5 minutes to determine the differencebetween the two samples. The difference (if any) will determine theexistence or lack of bacteria in the sample.

EXAMPLE 4

A differential reading could also be obtained by examining the change inabsorbance. This method could be done electronically wherein themetabolic activity of contaminants changes the indicator dye, and bystudying the difference in absorbance between the sample and thesample-derived negative control, any contamination can be detected.Traditionally, absorbance is done using a UV-Vis Spectrophotometer. Aquick way to measure absorbance is using a mobile phone. Once thechambers are filled with the sample and the sample-derived negativecontrol, the flash of the phone can be used as the light source whilethe phone camera can be the light sensor. By recording the dyeabsorbance change over a set amount of time and examining thedifference, contamination can be detected. Using absorbance to detectthe metabolic rate of viable cells will show the existence ofcontamination or the lack thereof but not concentration. Accordingly, itis useful in the field for a rapid, point-of-use measurement only.

EXAMPLE 5

By treating a contaminated sample with antibiotics, it is possible todetermine antibiotic susceptibility. The sample can be split in half andone half of it is treated with antibiotics. Monitoring the differentialrate allows the user to understand the effects of the antibiotic.Without the differential rate, it would only be possible to determinewhether the antibiotic kills (e.g., no growth) or does not kill. Withthe differential rate, it is possible to observe dose-response effects(e.g., a little antibiotic slow the growth a lot of antibiotic killsall). In this case the untreated sample serves as a positive control,and the sample that is treated is the test sample. Eventually, forantibiotic testing we will develop a triple chamber device, with thefirst chamber used for positive control (no antibiotic, cells andindicator are present), the second will be used for negative control(antibiotic and indicator, but no cells—achieved by filtering the samplevia 0.2 micron filter or centrifugation), and the third is the treatedsample (cells, indicator and antibiotic). This configuration would beuseful for antibiotics that may interact with the indicator. Thisfeature hasn't been described in publication but it was disclosed.

As introduced above, if the intent is to test more than one sample, thecassette can be adapted to include more chambers, as readily understoodby the person skilled in the art. Testing the efficacy of antibiotics isa good example of where a cassette with additional chambers will allowthe experimenter to test 2, 3, 4, 5, 10, 15, 20, 25 or more antibioticssimultaneously. The only requirement is that there be a chamber for eachantibiotic tested plus a chamber for the negative control.

Although the invention has been variously disclosed herein withreference to illustrative embodiments and features, it will beappreciated that the embodiments and features described hereinabove arenot intended to limit the invention, and that other variations,modifications and other embodiments will suggest themselves to those ofordinary skill in the art, based on the disclosure herein. The inventiontherefore is to be broadly construed, as encompassing all suchvariations, modifications and alternative embodiments within the spiritand scope of the claims hereafter set forth.

REFERENCES

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What is claimed is:
 1. A microfluidic cassette comprising: an inletchannel that splits into a sample channel and a sample-derived negativecontrol channel, wherein the sample channel is communicatively connectedto a sample chamber and the sample-derived negative control channel iscommunicatively connected to at least one sample-derived negativecontrol chamber, wherein the inlet channel comprises an inlet portupstream of the split, a first port downstream of the sample chamber,and a second port downstream of the sample-derived negative controlchamber(s), wherein the microfluidic cassette comprises a filter alongthe sample-derived negative control channel positioned between the splitand the sample-derived negative control chamber(s), and wherein themicrofluidic cassette further comprises a light barrier positionedbetween the sample chamber and the sample-derived negative controlchamber(s).
 2. The microfluidic cassette of claim 1, wherein thesample-derived negative control channel further comprises a secondsample-derived negative control chamber positioned between a firstsample-derived negative control chamber and the second port.
 3. Themicrofluidic cassette of claim 1, wherein each port comprises a septum.4. A kinetic fluorometer system, said system comprising: an excitationmodule comprising a light source and a voltage-controlled currentsource; the microfluidic cassette of claim 1; an excitation filtermounted between the light source and the microfluidic cassette; adetector positioned 90° relative to the excitation light path from thelight source; an emission filter positioned between the detector and themicrofluidic cassette; and a microprocessor.
 5. The system of claim 4,wherein the detector is a photometer to detect fluorescence intensity.6. The system of claim 4, wherein the system is compact, portable,and/or hand-held.
 7. The system of claim 4, wherein the detector detectschanges in fluorescence, absorbance, temperature, pressure, pH,conductivity and/or image processing.
 8. The system of claim 4, whereinthe microprocessor is present in a mobile phone, tablet, or computer. 9.The system of claim 4, wherein the light source is selected from thegroup consisting of an LED, laser-diode, electroluminescent lamp,incandescent lamp, halogen lamp, and sunlight.
 10. The system of claim4, wherein the sample chamber and the sample-derived negative controlchamber(s) have their own dedicated photometer.